ProtoClassify™

ProtoClassify™ is a tool for virtual screening requiring only 2D ligand information for input. The method uses Support Vector Machine technology to robustly classify known active compounds according to pharmacophoric features . It provides fast screening of the PCD, which currently contains >5 million commercially available compounds, or large custom virtual libraries.

ProtoClassify™ models were built and tested against a standard publically available QSAR test set. Performance of the models for various targets are shown in the following graphs:

ProtoClassify™ models can be built for any target for which a number of active molecules are known.

Classification models have been pre-built for over 20 targets of current pharmaceutical interest based upon analysis of existing ligands. Some of the prebuilt models are shown in the following table.

Classification Models Built

CCR1

PPARs

D1

S1P1

PDE4

Factor X

NPY1

COX-2

Androgen receptor

CDK-2

CB2

AA1A

Glucocorticoid

The speed of ProtoClassify™ enables screening of very large virtual libraries (up to 100 million compounds). It is thus suitable for screening large theoretical libraries. For example, ProtoClassify™ was used to create a model using ~20 known ligands for an aminergic GPCR. A 3 million PCD library set was screened from which only 10 compounds were selected for in vitro testing based on the model scores. Of these compounds 5 were active with a best Ki of 80 nM.